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Yorodumi- EMDB-10458: Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10458 | ||||||||||||
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Title | Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 1) | ||||||||||||
Map data | Sharpened EM map from Phenix Auto-Sharpen (unmasked) | ||||||||||||
Sample |
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Keywords | ribosome / SpeFL / arrest peptide / ornithine / protein synthesis | ||||||||||||
Function / homology | Function and homology information transcriptional attenuation by ribosome / regulation of translational elongation / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity ...transcriptional attenuation by ribosome / regulation of translational elongation / negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / negative regulation of translational initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||
Authors | Innis CA / Herrero del Valle A | ||||||||||||
Funding support | 3 items
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Citation | Journal: Nat Microbiol / Year: 2020 Title: Ornithine capture by a translating ribosome controls bacterial polyamine synthesis. Authors: Alba Herrero Del Valle / Britta Seip / Iñaki Cervera-Marzal / Guénaël Sacheau / A Carolin Seefeldt / C Axel Innis / Abstract: Polyamines are essential metabolites that play an important role in cell growth, stress adaptation and microbial virulence. To survive and multiply within a human host, pathogenic bacteria adjust the ...Polyamines are essential metabolites that play an important role in cell growth, stress adaptation and microbial virulence. To survive and multiply within a human host, pathogenic bacteria adjust the expression and activity of polyamine biosynthetic enzymes in response to different environmental stresses and metabolic cues. Here, we show that ornithine capture by the ribosome and the nascent peptide SpeFL controls polyamine synthesis in γ-proteobacteria by inducing the expression of the ornithine decarboxylase SpeF, via a mechanism involving ribosome stalling and transcription antitermination. In addition, we present the cryogenic electron microscopy structure of an Escherichia coli ribosome stalled during translation of speFL in the presence of ornithine. The structure shows how the ribosome and the SpeFL sensor domain form a highly selective binding pocket that accommodates a single ornithine molecule but excludes near-cognate ligands. Ornithine pre-associates with the ribosome and is then held in place by the sensor domain, leading to the compaction of the SpeFL effector domain and blocking the action of release factor 1. Thus, our study not only reveals basic strategies by which nascent peptides assist the ribosome in detecting a specific metabolite, but also provides a framework for assessing how ornithine promotes virulence in several human pathogens. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10458.map.gz | 1.3 GB | EMDB map data format | |
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Header (meta data) | emd-10458-v30.xml emd-10458.xml | 86.8 KB 86.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10458_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_10458.png | 70.3 KB | ||
Filedesc metadata | emd-10458.cif.gz | 15.1 KB | ||
Others | emd_10458_additional.map.gz emd_10458_half_map_1.map.gz emd_10458_half_map_2.map.gz | 165.4 MB 140.8 MB 140.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10458 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10458 | HTTPS FTP |
-Validation report
Summary document | emd_10458_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_10458_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_10458_validation.xml.gz | 23 KB | Display | |
Data in CIF | emd_10458_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10458 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10458 | HTTPS FTP |
-Related structure data
Related structure data | 6tc3MC 6tbvC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10458.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened EM map from Phenix Auto-Sharpen (unmasked) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.5335 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Post-processed map from RELION-3.0
File | emd_10458_additional.map | ||||||||||||
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Annotation | Post-processed map from RELION-3.0 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Odd EM half map
File | emd_10458_half_map_1.map | ||||||||||||
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Annotation | Odd EM half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Even EM half map
File | emd_10458_half_map_2.map | ||||||||||||
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Annotation | Even EM half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Escherichia coli ribosome-SpeFL complex stalled in response to L-...
+Supramolecule #1: Escherichia coli ribosome-SpeFL complex stalled in response to L-...
+Supramolecule #2: 50S subunit
+Supramolecule #3: 30S subunit
+Supramolecule #4: SpeFL peptide
+Supramolecule #5: Arg-tRNA located in the P-site
+Supramolecule #6: mRNA
+Macromolecule #1: 16S rRNA
+Macromolecule #22: 23S rRNA
+Macromolecule #23: 5S rRNA
+Macromolecule #54: mRNA
+Macromolecule #55: P-site Arg-tRNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #24: 50S ribosomal protein L2
+Macromolecule #25: 50S ribosomal protein L3
+Macromolecule #26: 50S ribosomal protein L4
+Macromolecule #27: 50S ribosomal protein L5
+Macromolecule #28: 50S ribosomal protein L6
+Macromolecule #29: 50S ribosomal protein L9
+Macromolecule #30: 50S ribosomal protein L31
+Macromolecule #31: 50S ribosomal protein L13
+Macromolecule #32: 50S ribosomal protein L14
+Macromolecule #33: 50S ribosomal protein L15
+Macromolecule #34: 50S ribosomal protein L16
+Macromolecule #35: 50S ribosomal protein L17
+Macromolecule #36: 50S ribosomal protein L18
+Macromolecule #37: 50S ribosomal protein L19
+Macromolecule #38: 50S ribosomal protein L20
+Macromolecule #39: 50S ribosomal protein L21
+Macromolecule #40: 50S ribosomal protein L22
+Macromolecule #41: 50S ribosomal protein L23
+Macromolecule #42: 50S ribosomal protein L24
+Macromolecule #43: 50S ribosomal protein L25
+Macromolecule #44: 50S ribosomal protein L27
+Macromolecule #45: 50S ribosomal protein L28
+Macromolecule #46: 50S ribosomal protein L29
+Macromolecule #47: 50S ribosomal protein L30
+Macromolecule #48: 50S ribosomal protein L32
+Macromolecule #49: 50S ribosomal protein L33
+Macromolecule #50: 50S ribosomal protein L34
+Macromolecule #51: 50S ribosomal protein L35
+Macromolecule #52: 50S ribosomal protein L36
+Macromolecule #53: SpeFL
+Macromolecule #56: MAGNESIUM ION
+Macromolecule #57: POTASSIUM ION
+Macromolecule #58: UNKNOWN ATOM OR ION
+Macromolecule #59: ZINC ION
+Macromolecule #60: L-ornithine
+Macromolecule #61: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Max: 100.0 K |
Details | Data were collected at the European Synchrotron Radiation Facility (ESRF CM01 cryo-electron microscope) |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 3620 / Average exposure time: 9.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -1.6 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |